Forensic Science International-Genetics最新文献

{"title":"Mitochondrial genome sequencing with ForenSeq™ mtDNA Whole Genome Kit","authors":"Jinfeng Xuan ,&nbsp;Guannan Long ,&nbsp;Haiduo Wu ,&nbsp;Ze Liu ,&nbsp;Biao Zhang ,&nbsp;Shaobo Yu ,&nbsp;Fu Ren ,&nbsp;Fei Guo","doi":"10.1016/j.fsigen.2025.103274","DOIUrl":"10.1016/j.fsigen.2025.103274","url":null,"abstract":"<div><div>Mitochondrial DNA (mtDNA) possesses unique genetic characteristics and plays a crucial role in forensic DNA analysis. Based on the massively parallel sequencing (MPS) technology alongside the short overlapping amplicon method, the ForenSeq™ mtDNA Whole Genome Kit is specifically designed for mtDNA analysis. In this study, we employ the ForenSeq™ mtDNA Whole Genome Kit on the MiSeq FGx® Sequencing System for mitochondrial genome (mtGenome) sequencing across nine consecutive runs and assess its MPS performance, such as read depth (RD), forward/reverse strand bias (SB), and mtGenome coverage. Furthermore, we conduct internal validations to evaluate its routine application in forensic sciences, including sensitivity, repeatability, concordance, degraded samples, inhibitor samples, case-type samples, and contamination. As a result, the Real-Time Analysis (RTA) and Universal Analysis Software (UAS) demonstrate proficient run metrics and MPS performance when 12–14 libraries are sequenced within a standard flow cell, achieving &gt; 80 % of reads passing filter, &gt; 80 % bases with ≥Q30, &gt; 5000 × of the average RD, ∼1.0 of the average SB, &gt; 70 % of the inter-amplicon balance, and &gt; 99 % of the mtGenome coverage. The five most vulnerable amplicons, exhibiting low RD and high SB, are identified as nucleotide positions (nps) 1094–1177, 5858–5975, 6109–6149, 6718–6810, and 7021–7090. For tertiary data analysis, the substitutions are accurately reported by UAS, while insertions and deletions (indels), point heteroplasmies (PHPs), and/or length heteroplasmies (LHPs) still necessitate manual inspection. On average, 40 variants were found in 60 samples, ranging from 27 to 54. A total of 2426 variants are observed at 491 nps. Moreover, the workflow can yield repeatable and reproducible results, generate complete mtGenome profiles from ≥ 2 pg input gDNA for high quality samples/control DNA or ≥ 0.5 cm hair shafts, and recover more/complete mtGenome information from severely degraded samples (degradation index &gt;10) and various types of case samples. If two rounds of purification are conducted, it can more effectively remove additional reaction components and enhance data recovery from the mtGenome, especially for low-input samples. The negative controls in three runs cover some reads, but these contaminations cannot compromise the mitochondrial analyses. In conclusion, the ForenSeq™ mtDNA Whole Genome Kit, including 234 short overlapping amplicons with an average size of 131 bp, can meet forensic needs on the whole mtGenome sequencing in real scenarios. In addition, the ten insights gained from this study may serve as a valuable reference for forensic scientists who are utilizing this kit.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103274"},"PeriodicalIF":3.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are microhaplotypes derived from the 1000 Genomes Project reliable for forensic purposes?","authors":"Yifan Wei ,&nbsp;Xi Li ,&nbsp;Qiang Zhu ,&nbsp;Tiantian Shan ,&nbsp;Haoyu Wang ,&nbsp;Xuan Dai ,&nbsp;Yufang Wang ,&nbsp;Ji Zhang","doi":"10.1016/j.fsigen.2025.103273","DOIUrl":"10.1016/j.fsigen.2025.103273","url":null,"abstract":"<div><div>Microhaplotypes (MHs) have emerged as an important genetic marker in forensic genetics. However, most studies have overlooked the potential for phasing errors within microhaplotypes based on the 1000 Genome Project (1kGP), which may impact the evaluation of various forensic parameters and lead to misleading results. In this study, we constructed a dense and extensive set of MHs across the human genome, using the expanded 1000 Genomes Project data aligned to GRCh38 reference genome. We applied three different SNP minor allele frequency (MAF) thresholds (0, 0.01, and 0.05) to evaluate the reliability of these markers. Utilizing pedigree data from 18 populations, which included a total of 602 trios, we scanned for and confirmed suspected phasing error events at these MH loci. We also sequenced 50 MHs for one trio of the Southern Han Chinese (CHS) population to further investigate these discrepancies. The results revealed the presence of phasing errors in MHs from 1kGP when analyzed using targeted enrichment and next-generation sequencing. The probability of suspected phasing error events was strongly and positively correlated with the effective number of alleles (Ae) and informativeness (In) of the markers. Additionally, these mismatch probabilities varied significantly across different continental populations. Additionally, when selecting loci, applying MAF filtering and avoiding regions such as the MHC can reduce the occurrence of such events to some extent. Based on these findings, we suggest that relying solely on sequencing data of the 1kGP for forensic purpose may be risky. A thorough investigation of the true forensic parameters of MHs is essential to ensure their reliability in forensic applications.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103273"},"PeriodicalIF":3.2,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanopore sequencing of MiniHap biomarkers for forensic DNA mixture deconvolution: A proof-of-principle study","authors":"Jian Zhang ,&nbsp;Xiaoting Mo ,&nbsp;Weiqiang Li ,&nbsp;Cheng Cheng ,&nbsp;Yu Feng ,&nbsp;Yiwen Zhang ,&nbsp;Shengbin Li","doi":"10.1016/j.fsigen.2025.103272","DOIUrl":"10.1016/j.fsigen.2025.103272","url":null,"abstract":"<div><div>Mixture deconvolution remains one of the major challenges in the field of forensic science. Currently, genetic markers are used and studied in the field of forensic genetics, including short tandem repeat (STR), insertion/deletion polymorphism (InDel), single nucleotide polymorphism (SNP), InDel closely linked to STR (DIP-STR), SNP closely linked to STR (SNP-STR), InDel closely linked to SNP (DIP-SNP) and microhaplotype (MH), all of which have been studied for DNA mixture analysis and have their own advantages and disadvantages. Mini-haplotype (MiniHap), as a novel haplotype genetic marker, contains 5 or more SNPs. A previous study has substantiated its significant high polymorphic characteristics, and it is expected to have potential applications in individual identification, paternity testing, ancestry inference, and mixture deconvolution. In this study, we first screened 22 MiniHaps with high polymorphism potential and constructed a panel based on the QNome nanopore sequencing device. Subsequently, we tested 100 unrelated Chinese Han individuals to evaluate the sequencing performance, allele (haplotype) frequencies, effective number of alleles (A_e) and forensic parameters of the 22 MiniHaps markers included in this novel assay. Next, a series of mixture simulations (two- or three-person mixtures with mixing ratios of 1:1–1:99 or 1:1:1–1:8:1) based on three standard materials (9947 A, 9948 and 2800 M) were detected by this MiniHap panel to explore its potential for DNA mixture deconvolution. The average A_e value was 10.9574, and 52.38 % of MiniHap loci had A_e values greater than 12.0000. The mean values of genetic diversity (GD) and power of discrimination (PD) were 0.8717 and 0.9457, respectively. Notably, most MiniHaps (85.71 %) had PD values exceeding 0.9000. The combined match probability (CMP) and combined power of exclusion (CPE) of this MiniHap panel were 4.4505 × 10⁻³¹ and 0.999999999999999996653, respectively. Moreover, the results of mixture analysis demonstrated that this MiniHap panel allowed detecting the components of minor contributor (s) even in imbalanced mixture samples, with detection limits of 1:39 and 1:8:1 for two- and three-person mixtures, respectively. In summary, MiniHap markers have remarkable application potential in mixture deconvolution, and it is necessary to conduct in-depth research on MiniHap markers for mixture analysis in the future.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103272"},"PeriodicalIF":3.2,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143644191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unprecedented male relative differentiation with Y-SNVs from whole genome sequencing","authors":"Dion Zandstra ,&nbsp;Arwin Ralf ,&nbsp;Zeliha Ozgur ,&nbsp;Wilfred F.J. van IJcken ,&nbsp;Mohsen Ghanbari ,&nbsp;Manfred Kayser","doi":"10.1016/j.fsigen.2025.103265","DOIUrl":"10.1016/j.fsigen.2025.103265","url":null,"abstract":"<div><div>The principal limitation of forensic Y-STR analysis, which identifies a male lineage rather than an individual man, is being addressed by the discovery and application of rapidly mutating Y-STRs (RM Y-STRs). Due to their higher mutation rates compared to standard Y-STRs used in forensics, RM Y-STRs significantly enhance the ability to differentiate between male relatives. However, some male relatives – particularly closely related ones – remain indistinguishable. Given the design and execution of the two previous RM Y-STR searches that discovered the 26 currently known RM Y-STRs, it is unlikely that future searches will largely increase the number of RM Y-STRs. To address the ongoing forensic challenge of differentiating between male relatives using Y chromosome analysis, this study explorers an alternative approach: Y-chromosomal singe nucleotide variants (Y-SNVs) obtained via whole genome sequencing (WGS). To assess the feasibility of the WGS technology in differentiating closely and distantly related males, we sequenced DNA samples of 24 male individuals belonging to three deep-rooted pedigrees, covering 12 father-son pairs and 72 pairs of distant male relatives separated by 8–15 meioses. Among the 76 meioses analyzed in total, 90 male relative-differentiating Y-SNVs were identified across the approximately 25 Mbp Y chromosome sequence generated per sample. A total of 141 male relative-differentiating Y chromosome mutations were observed when also considering Y-STRs from Yfiler Plus, RMplex, and WGS analyses. Of the 12 father-son pairs, six (50 %) were differentiated by one or more Y-SNVs, and 9 (75 %) with WGS and CE methods combined. All of the 72 pairs of distant male relatives were distinguished both through Y-SNVs and RM Y-STRs. Overall, when compared to RMplex, WGS yielded a 1.7-fold increase in the number of observed mutations in father-son pairs and a 4-fold increase in distantly related males. Our proof-of-principle study demonstrates (i) the feasibility and high value of Y-SNV markers and WGS technology in differentiating both close and distant male relatives; (ii) the superior performance of Y-SNVs from WGS relative to the previously used RM Y-STR markers and RMplex method; and (iii) the enhanced male relative differentiation achieved by combining both marker types and methods. We envision WGS as the method of choice for maximizing male relative differentiation based on Y chromosome information in high-profile criminal cases with male suspects where no autosomal STR profiles are available and where standard Y-STR and RM Y-STR analyses fail to distinguish the suspect from his male paternal relatives.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103265"},"PeriodicalIF":3.2,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse","authors":"Mirna Ghemrawi ,&nbsp;Andrea Ramírez Torres ,&nbsp;Michael Netherland Jr. ,&nbsp;Ying Wang ,&nbsp;Nur A. Hasan ,&nbsp;Bassam El-Fahmawi ,&nbsp;George Duncan ,&nbsp;Bruce McCord","doi":"10.1016/j.fsigen.2025.103266","DOIUrl":"10.1016/j.fsigen.2025.103266","url":null,"abstract":"<div><div>The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103266"},"PeriodicalIF":3.2,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic predictions of eye and hair colour in the Danish population","authors":"Amaia Cabrejas-Olalla ,&nbsp;Frank G. Jørgensen ,&nbsp;Jade Y. Cheng ,&nbsp;Peter C. Kjærgaard ,&nbsp;Mikkel H. Schierup ,&nbsp;Thomas Mailund ,&nbsp;Georgios Athanasiadis","doi":"10.1016/j.fsigen.2025.103267","DOIUrl":"10.1016/j.fsigen.2025.103267","url":null,"abstract":"<div><div>Genetic predictions of eye and hair colour are prominent examples of forensic DNA phenotyping that can help resolve criminal cases. The advent of high-throughput genotyping technologies in forensic genetics opens up the possibility of applying polygenic risk scores in forensic settings. In this work, we compare the performance of HIrisPlex with PRSice-2 in predicting eye and hair colour to gain insights into the relative benefits of new approaches. Predictions were carried out on 584 Danish high school students for which genetic and self-reported phenotype data were available. Prediction of brown eye colour was very accurate (AUC = 0.98), followed by blue eye colour (AUC = 0.82), while it failed for intermediate eye colour (AUC = 0.57). As for hair colour, red and black were overall better predicted than blond and brown, and PRSice-2 performed better in all but the black hair colour. Despite the limitations of the study, HIrisPlex exhibited its usual high performance in the prediction of brown and blue eye colour, as well as red and black hair colour. However, PRSice-2 offered overall improvements in hair colour prediction over HIrisPlex suggesting that there is room for improvement in forensic DNA phenotyping by using polygenic risk scores.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103267"},"PeriodicalIF":3.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143577906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species level and SNP profiling of skin microbiome improve the specificity in identifying forensic fluid and individual","authors":"Litao Huang ,&nbsp;Jieyu Du ,&nbsp;Linying Ye ,&nbsp;Yangyang Zheng ,&nbsp;Xueyuan Liu ,&nbsp;Enping Huang ,&nbsp;Jiaqian Le ,&nbsp;Xuan Huang ,&nbsp;Weian Du ,&nbsp;Chao Liu ,&nbsp;Ling Chen","doi":"10.1016/j.fsigen.2025.103256","DOIUrl":"10.1016/j.fsigen.2025.103256","url":null,"abstract":"<div><div>Human skin possesses individual and body fluid-specific microbial signatures potentially useful for forensic identification. Previous studies mostly attribute individuals based on the relative abundance of microbiota at single time point, however fluctuations in taxonomy and phylogenetic structure may cause this to be unreliable. In this study, we assessed the skin microbiome of individuals at consecutive time-point from fingers, palm, arm and forehead sites using full-length 16S rRNA gene sequencing. At the species level, hand samples (fingers, palm, arm) differed significantly from forehead microbes. Additionally, skin flora of the present study differed significantly from the dominant species that have been reported for saliva, feces, and vaginal secretions samples. ANOSIM analysis of all skin samples showed that inter-individual differences were greater than intra-individual differences, yet accuracy of individual identification was only 52.5 %. At the microbial gene level, three machine learning models based on single nucleotide polymorphism (SNP) profiles of <em>Cutibacterium acnes</em> resulted in accurate classification of more than 97.5 % individuals. These results indicate that consideration of bacterial SNP profiling may provide new directions for forensic identification and may have potential applications in body fluid identification and individual identification in forensic.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103256"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143592013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ReAct project: Bayesian networks for assessing the value of the results given activity level propositions","authors":"Peter Gill,&nbsp;Tacha Hicks,&nbsp;Angel Carracedo","doi":"10.1016/j.fsigen.2025.103223","DOIUrl":"10.1016/j.fsigen.2025.103223","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"76 ","pages":"Article 103223"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “A preliminary report on the exploration of salivary bacterial diversity by the multiplex SNaPshot assay” [Forensic Sci. Int.: Genet. 70 (2024) 103032]","authors":"Shuangshuang Wang ,&nbsp;Feng Song ,&nbsp;Xiangnan Guo ,&nbsp;Liya Gu ,&nbsp;Weijia Tan ,&nbsp;Peiyan Wu ,&nbsp;Weibo Liang ,&nbsp;Haibo Luo ,&nbsp;Yanyun Wang","doi":"10.1016/j.fsigen.2025.103227","DOIUrl":"10.1016/j.fsigen.2025.103227","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"76 ","pages":"Article 103227"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forensic Science International: Genetics: Past, present, and future of the journal and the field","authors":"Angel Carracedo","doi":"10.1016/j.fsigen.2025.103255","DOIUrl":"10.1016/j.fsigen.2025.103255","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"79 ","pages":"Article 103255"},"PeriodicalIF":3.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}